Modified Primers for Nucleic Acid Amplification and Detection

ABSTRACT

A method of nucleic acid amplification involving using a first modified primer which provides protection to the amplification product from exonuclease degradation and a second primer. The method provides a double stranded nucleic acid, one strand of which is degraded by a double strand nucleic acid specific exonuclease to form a single stranded nucleic acid, which is protected from exonuclease degradation.

TECHNICAL FIELD

The invention relates to methods for detecting the presence ofparticular nucleic acids in a sample.

BACKGROUND ART

Methods for amplifying nucleic acids are well known in the art.

The detection of amplified nucleic acid products may be carried out in anon-specific way which merely detects the presence of double strandednucleic acid (for example, by use of a double stranded-DNA intercalatingdye such as ethidium bromide or SYBR-green). Alternatively, asemi-specific detection of product may be carried out by resolvingapproximate molecular weight of the product, for example, by carryingout an electrophoresis of the reaction products prior to detection.Alternatively, there are a number of sequence-specific detection methodswhich typically involve the hybridization of a sequence-specific nucleicacid probe to the amplified region or which measure the degradation ofthe probe concomitant with the amplification of the target sequence andmake use of the nucleic acid exonuclease activity of the nucleic acidpolymerase.

A problem associated with detection of amplified PCR products usingsequence-specific probes is due to the fact that PCR produces doublestranded amplified products. Therefore in order for a sequence-specificprobe to be able to hybridise to the strand of the amplified product towhich it is complementary, the strands of the double stranded amplifiedproduct must be separated before hybridisation can occur. In order forthe sequence specific probe to be capable of displacing thecomplementary strand of the amplified product, it is possible toincrease the concentration of the probe in the detection mixture.However, using high concentrations of probe in the detection mixtureincreases the noise and as a result decreases the signal to noise ratio.

One way of circumventing the problems associated with the production ofa double stranded amplification product is to use the method known inthe art as asymmetric nucleic acid amplification, such as asymmetricPCR. Asymmetric PCR involves using unequal primer concentrations, i.e.one of the primers is present in excess, and the other primer of theprimer pair is not present in excess. The amplification producttherefore comprises predominantly the strand of the amplificationproduct which relates to an extended version of the primer that ispresent in excess.

However, it is known in the art that asymmetric PCR is less efficientthan symmetric or balanced PCR in which the concentration of the forwardand reverse primers is equal. This is due to the fact that once theprimer that is not present in excess is used up, the primer that is inexcess forms a single stranded product with linear rather thanexponential reaction kinetics.

An object of the invention is therefore to provide a method foramplifying a nucleic acid which provides an increased signal to noiseratio without compromising the efficiency of the detection method.

DISCLOSURE OF THE INVENTION

The inventors have provided a novel amplification method as shown inFIG. 1. In the amplification method, one of the two primers comprises atleast one modified nucleotide (see FIG. 1a ). Amplification of thetarget nucleic acid proceeds between the two primers, to provide adouble stranded nucleic acid amplification product. The first primerhaving at least one modified nucleotide (also referred to as “a modifiedprimer”) is extended to produce a first strand including the modifiednucleotide. The second primer is extended to produce a second strand(see FIG. 1b ). A 5′ to 3′ exonuclease is then provided which isspecific for double stranded nucleic acids and which is capable ofhydrolysing the second strand but is incapable of hydrolysing the firststrand in the region of the at least one modified nucleotide. Thereforethe amplified region of the first strand is not hydrolysed by theexonuclease. Therefore a single stranded nucleic acid comprising atleast the amplified region of the first strand is provided (see FIG. 1c). This single stranded nucleic acid is protected from exonucleasedegradation by virtue of the modified nucleotides included in it.

The single stranded nucleic acid may be detected by performing furthersteps which provide an increased signal to noise ratio. A labelled probewhich specifically hybridises with the single stranded nucleic acid ofFIG. 1c is added to the mixture. This probe binds to the single strandednucleic acid to form a double stranded nucleic acid (see FIG. 1d ). Thesame 5′ to 3′ exonuclease (although a different one could be used) isthen used to hydrolyse the probe. The hydrolysis of the probe releasesthe label, causing a detectable change to occur to the label which cansubsequently be detected (see FIG. 1e ). The fact that the exonucleasehydrolyses the probe but not the single stranded nucleic acid (which isprotected from exonuclease degradation) allows further probe moleculesto hybridise to the single stranded nucleic acid, subsequently providinga detectable change in the signal from the label. Therefore, each singlestranded nucleic acid produced can provide multiple signals, therebyincreasing the signal to noise ratio compared to using an amplificationmethod using two unmodified primers.

The invention therefore provides a nucleic acid amplification methodcomprising steps of:

-   -   a) performing nucleic acid amplification on a sample, using a        first primer including at least one modified nucleotide        (“modified primer”) and a second primer, wherein the        amplification provides a double stranded nucleic acid comprising        a first strand comprising the modified primer and a downstream        amplified region; and a second strand; and    -   b) incubating the double stranded nucleic acid of a) with a 5′        to 3′ double stranded nucleic acid specific exonuclease which        hydrolyses the second strand but does not hydrolyse the        amplified region of the first strand, to provide a single        stranded nucleic acid comprising the amplified region of the        first strand.

Surprisingly, the inventors have found that the method of the inventionis capable of producing a single stranded amplification product, whichallows for easy detection. The method of the invention does not sufferfrom the disadvantages such as inefficiency that are associated withother amplification methods which result in a single stranded nucleicacid product, e.g. asymmetric PCR.

Usually, step a) is performed a number of times (e.g. multiple PCRcycles) before step b) is performed. Thus the hydrolysis of step b) isdelayed until significant amplification has occurred, e.g. amplificationof at least 1000-fold.

The amplification method may further comprise steps of:

-   -   c) incubating the product of b) with a probe including a label,        wherein the probe specifically hybridises to the single stranded        nucleic acid;    -   d) incubating the product of c) with a 5′ to 3′ double stranded        nucleic acid specific exonuclease which hydrolyses the probe but        does not hydrolyse the amplified region of the first strand,        wherein hydrolysis of the probe leads to a detectable change in        the signal from the label; and    -   e) detecting the change.

Surprisingly, the inventors have found that the method of the inventioncan be used to detect the presence of the single stranded nucleic acidand simultaneously achieve an increased signal to noise ratio. The factthat the exonuclease hydrolyses the probe but not the single strandednucleic acid allows further probe molecules to hybridise to the singlestranded nucleic acid one after another providing an increased signal.Each single stranded nucleic acid that is produced during theamplification step can therefore provide multiple signals and thereforecan be detected numerous times. Hydrolysis of the probe can cause theenvironment of the label to change. The label is no longer attached tothe full length probe, and is instead free, or attached to a singlenucleotide or short part of the probe. This change in environment of thelabel leads to a change in the signal from the label. The change insignal from the label can be detected to detect the presence of thenucleic acid of interest.

The invention also provides a kit comprising a modified primer having atleast one modified nucleotide; and an exonuclease, wherein theexonuclease is a 5′ to 3′ double stranded nucleic acid specificexonuclease.

Where dUTP is used in PCR instead of dTTP, uracil is incorporated intothe first strand and the second strand during amplification. When aseries of amplification reactions are performed, uracyl-N-glycosylase(UNG) may be added prior to amplification to ensure that any carry-overcontamination occurring following a previous amplification is removedwhilst leaving any sample DNA unaffected (as these contain thyminerather than uracil), reducing the occurrence of false positive results.The inventors have shown that modified primers may be used to produce asingle stranded nucleic acid without interfering with activity of UNGprior to amplification.

The invention therefore also provides a nucleic acid amplificationmethod comprising steps of:

-   -   i. incubating a sample with uracil-N-glycosylase; and    -   ii. performing nucleic acid amplification on the product of i.        using a first primer including at least one modified nucleotide        (“modified primer”), a second primer, and dUTP in the absence of        dTTP, wherein the amplification provides a double stranded        nucleic acid comprising a first strand comprising the modified        primer and a downstream amplified region; and a second strand.

The method may further comprise a step of:

-   -   iii. incubating the double stranded nucleic acid of ii. with a        5′ to 3′ double stranded nucleic acid specific exonuclease which        hydrolyses the second strand but does not hydrolyse the        amplified region of the first strand, to provide a single        stranded nucleic acid comprising the amplified region of the        first strand.

The method may further comprise the steps of:

-   -   iv. incubating the product of iii. with a probe including a        label, wherein the probe specifically hybridises to the single        stranded nucleic acid;    -   v. incubating the product of iv. with a 5′ to 3′ double stranded        nucleic acid specific exonuclease which hydrolyses the probe but        does not hydrolyse the amplified region of the first strand,        wherein hydrolysis of the probe leads to a detectable change in        the signal from the label; and    -   vi. detecting the change.

The invention also provides a kit comprising a modified primer having atleast one modified nucleotide, dUTP and UNG. The kit may also include anexonuclease, wherein the exonuclease is a 5′ to 3′ double strandednucleic acid specific exonuclease.

The kits of the invention may be used to perform the methods of theinvention.

Nucleic Acid Amplification

Nucleic acid amplification may be performed using any method known inthe art, including the polymerase chain reaction (PCR), the ligase chainreaction (LCR)¹, strand displacement amplification (SDA)², transcriptionmediated amplification³, nucleic acid sequence-based amplification(NASBA)⁴, Helicase-dependent amplification⁵ and loop-mediated isothermalamplification⁶.

A standard amplification mixture for PCR comprises: a first primer and asecond primer wherein the two primers are complementary to the 3′ endsof each of the sense and antisense strand of the target nucleic acid, athermostable DNA polymerase, e.g. Taq polymerase isolated from thethermophilic bacterium, Thermus aquaticus, deoxynucleoside triphosphates(dNTPs), buffer solution, divalent cations, e.g. magnesium or manganeseions, and monovalent cations, e.g. potassium ions.

Alternative thermostable DNA polymerases are, Pfu polymerase isolatedfrom Pyrococcus furiosus which has a proof reading activity absent fromTaq polymerase and is therefore a higher fidelity enzyme.

As mentioned above, dUTP may be used instead of dTTPs. Where dUTPs areused, UNG may be added to the sample prior to amplification to removeany carry-over contamination (e.g. that is present in the environmentdue to leakage from a previous experiment) without affecting the nucleicacids present in the sample.

Uracil-N-glycosylase (UNG) is also abbreviated in the art to UDG. AnyUNG may be used in the methods of the invention which is capable ofhydrolysing DNA including uracil. For example, the UNG used in themethods and kits of the invention may be human UNG or E. coli UNG.

Where a series of amplification reactions are performed using dUTPs,using UNG allows carry-over contamination between separate reactions tobe reduced. Any leaked amplified product that becomes present in thesample can be removed using UNG prior to amplification. The nucleic acidamplification of the present invention uses a first primer having atleast one modified nucleotide and a second primer. The at least onemodified nucleotide is incorporated into the first strand of the doublestranded nucleic acid amplification product. As described below thenucleotide modification may be any modification which is not susceptibleto hydrolysis by the exonuclease of the invention. The first primerhaving at least one modified nucleotide may be either the forward primeror the reverse primer. This first strand which includes the modifiedprimer is also the strand to which the probe used in the presentinvention is capable of specifically hybridising. The second primer isincorporated into the second strand of the double stranded nucleic acidamplification product.

The second primer can be hydrolysed by the exonuclease. As a consequencethe second strand which is produced as a result of amplification of thesecond primer can be hydrolysed by the exonuclease.

The nucleic acid amplification used in the invention may be symmetricnucleic acid amplification, e.g. symmetric PCR, i.e. the forward andreverse primers may be present at substantially the same concentration.Alternatively the nucleic acid amplification used in the invention maybe asymmetric nucleic acid amplification e.g. asymmetric PCR, i.e. oneof the primers is present in excess, and the other primer is not presentin excess. The methods of the invention provide high signal to noiseratio even when symmetric nucleic acid amplification such as symmetricPCR is used in favour of asymmetric nucleic acid amplification suchasymmetric PCR.

Amplification Products

The amplification products are the nucleic acids formed from the nucleicacid amplification step of the present invention. The nucleic acidamplification of the invention provides double stranded nucleic acids asamplification products. Preferably the nucleic acid amplificationprovides predominantly double stranded amplification products. Doublestranded nucleic acids as amplification products are generally theresult of symmetric nucleic acid amplification such as symmetric PCR.Alternatively, the nucleic acid amplification may provide a lower amountof double stranded amplification products amongst predominantly singlestranded nucleic acids as amplification products. Single strandednucleic acids as amplification products are generally the result ofasymmetric nucleic acid amplification such as asymmetric PCR.

Double stranded amplification products that are formed in the nucleicacid amplification step of the present invention comprise a first strandand a second strand. The first strand is formed by extension of thefirst primer and the second strand is formed by extension of the secondprimer. The at least one modified nucleotide of the first primer istherefore retained in the first strand. The region downstream of thefirst primer in the first strand is the downstream amplified region. Dueto the presence of the at least one modified nucleotide in the firstprimer, the downstream amplified region cannot be hydrolysed by theexonuclease.

The second strand preferably does not include any modified nucleotidesthat cannot be hydrolysed by the exonuclease. The second primer isextended during nucleic acid amplification to form the second strand.

Both the first strand and the second strand may comprise modificationswhich do not affect the hydrolysis of the strand by the exonucleasesused in the present invention.

Modified Nucleotide

The first primer comprises at least one modified nucleotide. A modifiednucleotide may be any nucleotide which comprises at least one modifiedsugar moiety, at least one modified internucleoside linkage and/or atleast one modified nucleobase, wherein the modification prevents thenucleotide from being hydrolysed by the exonuclease of the presentinvention. A modified nucleotide comprises at least one modificationcompared to naturally occurring RNA or DNA nucleotide.

The at least one modified nucleotide may comprise at least one modifiedsugar moiety. The modified sugar moiety may be a 2′-O-methyl sugarmoiety. The modified sugar moiety may be a 2′-O-methoxyethyl sugarmoiety. The modified sugar may be a 2′fluoro modified sugar. As analternative, the modified sugar moiety may be a bicyclic sugar. Bicyclicsugars include 4′-(CH₂)n-O-2′ bridges, wherein n is 1 or 2; and4′-O—CH(CH₃)—O-2′ bridges.

The at least one modified nucleotide may comprise at least one modifiedinternucleoside linkage. The at least one modified internucleosidelinkage may be at least one phosphoramidite linkage. The at least onemodified internucleoside linkage may be at least one phosphorothioatelinkage.

The at least one modified nucleotide may comprise at least one modifiednucleobase.

The at least one modified nucleotide may comprise more than onemodification, e.g. a modified nucleotide may comprise a modified sugarmoiety and a modified internucleoside linkage. Alternatively, themodified nucleotide may comprise a modified sugar moiety and a modifiednucleobase, or a modified internucleoside linkage and a modifiednucleobase. The modified nucleotide may comprise a modified sugarmoiety, a modified internucleoside linkage and a modified nucleobase.

The at least one modified nucleotide may be present at any position inthe first primer. For example the at least one modified nucleotide maybe present at the 5′ end of the first primer, or may be present at the3′ end of the first primer, or may be present in the central section ofthe first primer, or may be interspersed throughout the first primer.Usually, the at least one modified nucleotide is present at the 5′ endof the primer. Where a modified nucleotide comprises a modifiedinternucleoside linkage at the 5′ end of the primer, the internucleosidelinkage between the first and second nucleotide is modified.

The modified primer may comprise multiple modified nucleotides. Forexample, the modified primer may comprise at least 2, at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9 orat least 10 modified nucleotides. Specifically, the modified primer maycomprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, or more than 20 modified nucleotides. Each of the nucleotides ofthe modified primer may be modified nucleotides.

Where the modified primer comprises multiple modified nucleotides, themodified nucleotides may be contiguous nucleotides in the primer. As analternative, the modified nucleotides may be spaced out along theprimer, i.e. one or more unmodified nucleotides may be present inbetween the modified nucleotides. The spaces of unmodified nucleotidesmay comprise, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more unmodifiednucleotides. Preferably, the modified nucleotides are contiguousnucleotides.

Preferably, the first primer comprises 3 or 4 modified nucleotides.Preferably, the first primer comprises 3 or 4 contiguous modifiednucleotides. Preferably, the first primer comprises 3 or 4 contiguousmodified nucleotides at the 5′ end. Preferably, the 3 or 4 modifiednucleotides comprise phosphorothioate linkages. In some embodiments, thefirst primer comprises three contiguous phosphorothioate linkages at the5′ end, i.e. the linkages between the first and second, second and thirdand third and fourth nucleotides are phosphorothioate linkages. In someembodiments, the first primer comprises four contiguous phosphorothioatelinkages at the 5′ end, i.e. the linkages between the first and second,second and third, third and fourth and fourth and fifth nucleotides arephosphorothioate linkages.

Primer

As mentioned above, the methods of the invention use a first primer anda second primer. The first primer may be the forward primer and thesecond primer may be the reverse primer. Alternatively, the secondprimer may be the forward primer and the first primer may be the reverseprimer. The first primer comprises at least one modified nucleotide. Thenucleic acid amplification step of the invention causes the modifiedprimer to be extended to form the first strand in the double strandednucleic acid amplification product. The invention also provides specificmodified primers and pairs of primers, as described below.

A primer used in the methods and kits of the invention will generally beat least 10 nucleotides long, e.g. the primer may be 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides inlength. The primer can be fully complementary to its target, but in someembodiments (e.g. in TMA) a primer can include a first region which iscomplementary to its target and a second region which is not. Shorterprobe lengths are favoured if the GC content of the probe is high. Thelength of the first primer includes the at least one modifiednucleotide.

In one embodiment, the first primer and the second primer are capable ofamplifying a Chlamydia trachomatis nucleic acid sequence. The firstprimer may comprise the nucleotide sequence ofA*G*A*T*TCCAGAGGCAATGCCAAAGAAA (SEQ ID NO: 1) orA*G*A*TTCCAGAGGCAATGCCAAAGAAA.

N* indicates that the nucleotide at the specified position is a modifiednucleotide. Where the modified nucleotide N*comprises a modifiedinternucleoside linkage the modified internucleoside linkage is betweenthe specified nucleotide and the next nucleotide in the 3′ direction.

Therefore, the first primer may comprise the nucleotide sequence of SEQID NO: 1, wherein nucleotides 1-3 or 1-4 are modified nucleotides. Thenucleotides of the primer are numbered from the 5′ end. Thereforenucleotides 1-3 or 1-4 are the 3 or 4 nucleotides at the 5′ end of theprimer. The modified nucleotides may comprise phosphorothioate linkages.

As an alternative, the first primer may comprise the nucleotide sequenceof G*T*T*T*GGACACTAGTCAGCATCAAGCTAGG orG*T*T*TGGACACTAGTCAGCATCAAGCTAGG, i.e. the first primer may comprise thenucleotide sequence of SEQ ID NO: 2, wherein nucleotides 1-3 or 1-4 aremodified nucleotides. The modified nucleotides may comprisephosphorothioate linkages. The invention also provides pairs of primerscomprising a first primer comprising SEQ ID NO: 1, wherein nucleotides1-3 or 1-4 are modified nucleotides optionally comprisingphosphorothioate linkages, and a second primer comprising SEQ ID NO: 2,wherein SEQ ID NO: 2 is unmodified, i.e. comprises no modifiednucleotides.

The invention also provides pairs of primers comprising a first primercomprising SEQ ID NO: 2, wherein nucleotides 1-3 or 1-4 are modifiednucleotides optionally comprising phosphorothioate linkages, and asecond primer comprising SEQ ID NO: 1, wherein SEQ ID NO: 1 isunmodified, i.e. comprises no modified nucleotides.

Sample

The sample is a composition on which the method of the invention isperformed in order to determine whether a nucleic acid of interest ispresent. The sample may be a composition in which the nucleic acid to bedetected is suspected to be present, or may be a composition in whichthe nucleic acid to be detected is potentially present. The nucleic acidof interest is capable of being amplified by the first primer and thesecond primer.

The sample may be material obtained from an animal or plant. The samplemay be a cellular sample. The sample may be obtained with minimalinvasiveness or non-invasively, e.g., the sample may be obtained from ananimal using a swab, or may be a bodily fluid. As an alternative, thesample may be material obtained from food or water. One skilled in theart will appreciate that samples can be diluted prior to the analysis oflevels of compounds. Preferably, the sample is obtained from a genitalswab, e.g. a vaginal swab.

The sample may have been treated since being obtained from the subject.For example, one skilled in the art will appreciate that samples can bepurified, e.g. to purify nucleic acids, diluted, concentrated,centrifuged, frozen, etc. prior to target detection.

An animal may be a vertebrate or non-vertebrate animal. Vertebrateanimals may be mammals. Vertebrate mammals may be human. Examples ofmammals include but are not limited to mouse, rat, pig, dog, cat,rabbit, primate or the like. The subject may be a primate. Preferablythe subject is human.

Nucleic Acid of Interest

The nucleic acid of interest is the nucleic acid which the method of theinvention intends to detect the presence or absence of. The nucleic acidof interest comprises the amplicon that is amplified by the nucleic acidamplification. The primers used in the nucleic acid amplificationreaction hybridise to the nucleic acid of interest.

The nucleic acid of interest may be a nucleic acid that is specific to aparticular pathogen, e.g. to a virus, a bacterium or a fungus. Thenucleic acid may therefore be detected in a sample from an animal inorder to diagnose a particular disease in an animal.

The nucleic acid may be specific to one of the following pathogens:Trichomonas vaginalis, Neisseria gonhorroeae, Chlamydia trachomatis,mycoplasma genitalium or methicillin resistant Staphylococcus aureus.

As an alternative, the nucleic acid may be a sequence endogenous to thesubject from which the sample is obtained. The nucleic acid may be amarker for a particular characteristic or a particular predisposition.In this situation, the method of the invention may detect thepredisposition of a subject from which a sample is taken to developing aparticular disease. As a further alternative, the method of theinvention may be used to determine the presence or absence of aparticular polymorphism in a subject, e.g. in comparison to anothersubject, in order to determine similarities and differences betweensubjects.

Exonuclease

The exonuclease used in the present invention is capable of hydrolysingthe second strand of the double stranded nucleic acid amplificationproduct. The exonuclease is not capable of hydrolysing the amplifiedregion of the first strand of the double stranded amplification product.The exonuclease may be capable of hydrolysing part of the first strand,e.g. the 5′ end of the first primer if the at least one modifiednucleotide is not located at the 5′-terminal nucleotide. In embodimentswhere a probe is present, an exonuclease may be capable of hydrolysingthe probe.

The exonuclease of the invention is a 5′ to 3′ double stranded nucleicacid specific exonuclease. Double stranded nucleic acid specificexonucleases are used such that one strand of the double strandednucleic acids that are produced as amplification products of the nucleicacid amplification is broken down by hydrolysis from the 5′ end to the3′ end by an exonuclease. Where a probe is used, an exonuclease may alsobe used to break down the probe by hydrolysis from one end following itshybridisation to the first strand. In this step, the exonucleaseperforms the function of causing a detectable change in the labelfollowing hydrolysis of the probe, e.g. by changing the environment inwhich it is in, in such a way that may be detected in order to determinethe presence or absence of the nucleic acid of interest.

Preferably, the exonuclease that is used to hydrolyse the probe is thesame as the exonuclease used to hydrolyse the second strand.

The exonuclease may be any 5′ to 3′ double strand specific exonuclease.The exonuclease may be selected from the group consisting of a Thermusaquaticus 5′ to 3′ exonuclease, a T7 exonuclease, a lambda exonuclease,exonuclease V and a T5 exonuclease. Preferably, the exonuclease is a T7exonuclease.

Probe

The probe is capable of specifically hybridising to the first strand.The probe may hybridise to the entire length or a portion of the firststrand. The probe includes a label. Hydrolysis of the probe leads to adetectable change in the signal from the label. The detection of thechange allows for measurement of the presence or absence of the nucleicacid of interest. The entire probe may be capable of specificallyhybridising to the first strand. As an alternative, the probe mayinclude a nucleic acid that is capable of specifically hybridising tothe first strand.

Probes used in the invention are typically 15 to 45 nucleotides inlength, i.e. the probe may be 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44 or 45 nucleotides in length.

The probe can be fully complementary to its target, but in someembodiments the probe can include a first region which is complementaryto its target and a second region which is not.

The probe may include one or more additional moieties other than theregion capable of hybridising to the target sequence. The additionalmoieties may be additional nucleic acid sequences or be non-nucleic acidmoieties. For example, the probe may include a linker region whichattaches it to an array. The additional moiety may be a label moiety.Particular types of labels that may be used are described in more detailbelow.

Label

The probe and/or primers described above may be linked to a label toassist their detection. The label may be any label which provides asignal. The label may be radioactive, enzymatically active,fluorescently active, luminescently active, or electrochemically active.Hydrolysis of the probe leads to a detectable change in the signal fromthe probe. This change in the signal from the label may be due to achange in the environment of the label following hydrolysis of theprobe.

Where detection of multiple nucleic acid sequences are undertakensimultaneously, for example where two nucleic acids of interest areamplified and detected simultaneously or where detection of a nucleicacid of interest and detection of an internal control nucleic acidsequence are both undertaken simultaneously, the labels used to assistin the detection of the multiple nucleic acid sequences are preferablydistinguishable from each other, for example, they may be differentfluorophores or they may be different electrochemically active agents orelectrochemically active labels providing electrochemicallydistinguishable activity. As an alternative, the labels may be the sameand the detection of the separate nucleic acids may be undertaken inseparate detection chambers.

The present invention is especially suitable for use withelectrochemically labelled probes and/or primers. In particular, theelectrochemical label may include those comprising metallo-carbocyclicpi complexes, that is organic complexes with partially or fullydelocalized pi electrons. Suitable labels include those comprisingsandwich compounds in which two carbocyclic rings are parallel, and alsobent sandwiches (angular compounds) and monocyclopentadienyls.Preferably, the electrochemically active markers are metallocene labels.More preferably they are ferrocene labels. Where the label is anelectrochemical label, the detectable change in the signal from thelabel may be a change in the current which flows through the label onapplication of potential difference across the label. The label may be aferrocene label. Examples of labels which may be used in the methods ofthe invention can be found in WO03/074731, WO2012/085591 and WO2013/190328. The label may be a fluorescent label. For example, theferrocene label may have the structure of formula I in WO2012/085591. Asan alternative, the ferrocene label may have the structure of formula Iin WO 2013/190328.

General

The term “comprising” encompasses “including” as well as “consisting”e.g. a composition “comprising” X may consist exclusively of X or mayinclude something additional e.g. X+Y.

The term “specifically hybridises” has its customary meaning of capableof hybridising to the sequence of the intended target and not tosequences that are not present in the intended target.

Unless specifically stated otherwise, a process comprising a step ofmixing two or more components, or incubating two or more componentstogether does not require any specific order of mixing. Thus componentscan be mixed in any order. Where there are three components then twocomponents can be combined with each other, and then the combination maybe combined with the third component, etc.

Unless specifically stated otherwise, the steps of the methods of theinvention may be performed in any order.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Overview of the amplification method of the invention.

FIG. 2. Comparison of two C. trachomatis samples each amplified withstandard and modified reverse primer (3 and 4 modified bases).

FIG. 3. Amplification and detection of C. trachomatis target sequenceusing standard, 3-base modified and 4-base modified reverse primersusing semi-rapid and rapid PCR protocols. Error bars are +/−1 standarddeviation from the mean.

FIG. 4. Exclusivity data for standard and 4-base modified reverse primerwith 14 organisms using semi-rapid PCR of C. trachomatis targetsequence. Error bars are +/−1 standard deviation from the mean.

FIG. 5. Inclusivity data using standard and 4-base modified reverseprimers with 14 serovars using semi-rapid PCR of C. trachomatis targetsequence. Error bars are +/−1 standard deviation from the mean.

FIG. 6. Comparison of standard and 4-base modified reverse primers usinga range of C. trachomatis template concentrations and a consistentconcentration of internal control nucleic acid. Error bars are +/−1standard deviation from the mean.

FIG. 7. Boxplot of C. trachomatis peak heights obtained with standard(ABR114) and 4-base modified (ABR115) reverse primers (n=10 for alldetections) for outer chamber (CT1) and inner chamber (CT2) of acartridge.

FIG. 8. Amplification and detection of N. gonhorroeae target sequenceusing standard and 4-base modified forward and reverse primers usingsemi-rapid PCR.

FIG. 9. Amplification and detection of internal control nucleic acidusing standard and 4-base modified forward and reverse primers usingsemi-rapid PCR.

FIG. 10. Amplification and detection of Mycoplasma genitalium targetsequence using standard and 4-base modified forward and reverse primersusing semi-rapid PCR.

MODES FOR CARRYING OUT THE INVENTION

Comparison of Standard Primers and Modified Primers in C. trachomatisAssay

Reverse (Rv) primers with 3 and 4 consecutive phosphorothioatemodifications at the 5′ end were tested in several experiments togetherwith an unmodified forward (Fw) primer and compared to peak heightsobtained when using normal Rv and Fw primers together. Results areprovided in FIG. 2. In the C. trachomatis assay, an electrochemicallylabelled probe hybridises to the strand extended from the reverseprimer. Therefore, the reverse primer, rather than the forward primer ismodified to prevent degradation, i.e. the first primer is the reverseprimer and the second primer is the forward primer.

A substantial increase in electrochemical signal was observed when themodified Rv primers were used compared with standard Rv primers. Fourmodifications provided a larger increase in peak height than threemodifications. This increase was observed across a number of experimentsusing a range of template concentrations and amplification protocols.Experiments were also carried out to verify the system of primerprotection against nuclease degradation including the use of a modifiedFw primer.

This is due to the fact that a single-stranded product is produced whichis more amenable to probe hybridisation and therefore detection.Furthermore, the assay provides an increased signal by hydrolysing theprobe after it hybridises to the first strand, but not allowing thefirst strand to be hydrolysed because it is protected by the modifiednucleotides. In this way, multiple probe molecules are able to hybridiseto a single copy of the first strand providing an increased signal.

Compatibility of the Modified Rv Primer with Rapid Amplification

Unmodified Rv primers and 3-base modified and 4-base modified Rv primerswere used in amplification reactions with unmodified Fw primers. The PCRamplifications were performed using either a semi-rapid protocol(Baseline) or a rapid protocol (1-9 SLOW) in order to determine whetherthe modified primers could be used in the semi-rapid PCR protocol. Theresults of these experiments are provided in FIG. 3. All three primersets had undetectable peak heights in the negative controls. Substantialincreases in peak heights relative to the unmodified control wereobtained for both amplification protocols (semi-rapid and rapid), withthe Rv primer containing four modifications providing increased peakheights compared to three modifications. Therefore, modified primerswere found to be compatible with rapid PCR.

Effect of the Modified Rv Primer on the C. trachomatis Assay Inclusivityand Exclusivity.

It is known in the art that it is possible for phosphorothioatemodifications to affect a primer's annealing properties. Therefore anexperiment was carried out to assess any potential effects of using aphosphorothioate-modified Rv primer on the C. trachomatis assayinclusivity and exclusivity. A number of organisms were selected tocontain species that were clinically relevant, closely related to C.trachomatis and those that produced the highest signal outliers inprevious exclusivity experiments (using standard primers). This panelwas tested using both the standard unmodified Rv primer and the 4 basemodified Rv primer using semi-rapid amplification. The results of theseexperiments are provided in FIG. 4. To establish inclusivity, 14serovars of C. trachomatis were amplified using semi-rapid amplificationin the presence of the standard C. trachomatis Rv primer or the 4-basemodified Rv primer. The amplification products were detectedelectrochemically using electrochemically labelled probes. The resultsof these experiments are provided in FIG. 6. The data show that using Rvprimers with 4 modified bases at the 5′ end does not affect theexclusivity or the inclusivity of the assay.

Effect of the Modified Rv on Degradation of Carry-Over Amplicon by UNG

UNG (Uracyl-N-Glycosylase) together with dUTPs may be used in the C.trachomatis assay to prevent false negative results from carry-overcontamination by amplicon. It was tested whether use of modified primerswould affect the mechanism or ability of UNG to degrade carry-overcontamination.

Amplification using standard and 4 base modified C. trachomatis Rvprimer was carried out to generate test amplicon using dNTPs with dUTPinstead of dTTP. Following this, a dilution of each amplicon was used intwo subsequent PCRs (using standard Rv or a 4 base modified primer) inthe presence or absence of UNG. Following amplification, amplificationproducts were electrochemically detected.

The results demonstrate that whilst using the modified Rv primerproduces a greater electrochemical signal (as demonstrated above),amplification products containing the modified Rv primer are susceptibleto UNG degradation in the same way that amplification products producedusing the standard primer is. Therefore, using a C. trachomatis Rvprimer with 4 phosphorothioate nucleosides at the 5′ end does not affectthe ability of UNG to degrade carry-over contamination.

Compatibility of the Modified Rv with the Internal Control

The C. trachomatis assay uses an internal control which monitors theassay at each stage and verifies a negative result. Experiments wereperformed to test whether the use of a modified Rv primer adverselyaffected the amplification or detection of the internal control.

An experiment was carried out that amplified a serial dilution of a C.trachomatis template with a consistent amount of internal control usingstandard unmodified reverse primers and 4-base modified reverse primers.The two amplified nucleic acids were detected electrochemically. Resultsof these experiments are provided in FIG. 7. FIG. 7 shows that theinternal control is capable of being consistently amplified and detectedusing an assay involving standard unmodified Rv primer or modified Rvprimer in the presence of a range of C. trachomatis templates.Therefore, using a C. trachomatis Rv primer with 4 phosphorothioatenucleosides at the 5′ end does not affect the amplification or detectionof the internal control across a range of C. trachomatis templateconcentrations

Compatibility of the Modified Rv with the Integrated Cartridge

Cartridges were produced in which standard unmodified Rv primers(ABR114) or 4-base modified Rv primers (ABR115) were used to allow theperformance of the different primers to be assessed on integratedcartridges. Ten replicates of each of 500 IFU and 0 IFU samples percartridge type were amplified on the cartridge and detected in thecartridge using a cartridge reader. The results of these experiments areshown in FIG. 8 below. FIG. 8 shows that using the modified C.trachomatis Rv primer increased the mean peak height by ˜2.2 fold in theouter chamber of the cartridge and by ˜1.6 fold for the inner chamber ofthe cartridge for C. trachomatis positive samples compared to usingstandard unmodified primers. The 0 IFU samples were unaffected by themodified primer thereby increasing the signal-noise ratio.

Comparison of Standard Primers and Modified Primers in N. gonhorroeaeAssay

In order to determine the different effects of using differentcombinations of modified and unmodified primers, experiments wereperformed in which 1000 copies of N. gonhorroeae were amplified anddetected electrochemically. The results of these experiments are shownin FIG. 9.

In the N. gonhorroeae assay, the probe hybridises to the strand extendedfrom the forward primer. Therefore, the forward primer, rather than thereverse primer is modified to prevent degradation, i.e. the first primeris the forward primer and the second primer is the reverse primer. Whereboth forward and reverse primers are modified to include 4phosphorothioate nucleosides, both strands are protected fromdegradation by the exonuclease. This prevents the probe from hybridisingto the amplified target nucleic acid, resulting in a large signaldecrease.

Modifying the reverse primer rather than the forward primer means thatthe strand to which the probe binds is not protected from exonucleasedegradation but the other strand is protected from degradation.Therefore, the majority of copies of the strand to which the probe bindswill be degraded by exonuclease preventing hybridisation of the probe.

Using unmodified forward and reverse primers provides a control level ofamplification in the presence of the N. gonhorroeae target sequence.

Modifying the forward primer, but not the reverse primer at the 5′ endprovides protection from exonuclease degradation for the first strand towhich the probe binds, meaning that only the other strand is degraded.Probe is able to bind to the first strand, and the probe is degraded toprovide a signal. Degradation of the probe allows further probemolecules to bind to the first strand and provide an increased signal.This causes a substantial increase in the mean peak height compared tothe peak height when using unmodified primers.

Comparison of Standard Primers and Modified Primers in Assay forInternal Control

In order to determine the different effects of using differentcombinations of modified and unmodified primers, experiments wereperformed in which 100 pg of internal control nucleic acid was amplifiedand detected electrochemically. The results of these experiments areshown in FIG. 10.

In the internal control amplification reaction, the probe hybridises tothe strand extended from the reverse primer. Therefore, the reverseprimer, rather than the forward primer is modified to preventdegradation, i.e. the first primer is the reverse primer and the secondprimer is the forward primer. Where both forward and reverse primers aremodified to include 4 phosphorothioate nucleosides, both strands areprotected from degradation by the exonuclease. This prevents the probefrom hybridising to the amplified target nucleic acid, resulting in alarge signal decrease.

Modifying the forward primer rather than the reverse primer means thatthe strand to which the probe binds is not protected from exonucleasedegradation but the other strand is protected from exonucleasedegradation but the other strand is protected from degradation.Therefore, the majority of copies of the strand to which the probe bindswill be degraded by exonuclease preventing hybridisation of the probe.

Using unmodified forward and reverse primers provides a control level ofamplification in the presence of internal control nucleic acid.

Modifying the reverse primer, but not the forward primer at the 5′ endprovides protection from exonuclease degradation for the first strand towhich the probe binds, meaning that only the other strand is degraded.Probe is able to bind to the first strand, and the probe is degraded toprovide a signal. Degradation of the probe allows further probemolecules to bind to the first strand and provide an increased signal.This causes a substantial increase in the mean peak height compared tothe peak height when using unmodified primers.

Comparison of Standard Primers and Modified Primers in M. genitaliumAssay

In order to determine the different effects of using differentcombinations of modified and unmodified primers, experiments wereperformed in which varying copy numbers of M. genitalium were amplifiedand detected electrochemically. The results of these experiments areshown in FIG. 11.

In the M. genitalium assay, the probe hybridises to the strand extendedfrom the reverse primer. Therefore, the reverse primer, rather than theforward primer is modified to prevent degradation, i.e. the first primeris the reverse primer and the second primer is the forward primer. Whereboth forward and reverse primers are modified to include 4phosphorothioate nucleosides, both strands are protected fromdegradation by the exonuclease. This prevents the probe from hybridisingto the amplified target nucleic acid, resulting in a large signaldecrease.

Using unmodified forward and reverse primers provides a control level ofamplification in the presence of M. genitalium target sequence.

Modifying the reverse primer, but not the forward primer at the 5′ endprovides protection from exonuclease degradation for the strand to whichthe probe binds, meaning that only the other strand is degraded. Probeis able to bind to the first strand, and the probe is degraded toprovide a signal. Degradation of the probe allows further probemolecules to bind to the first strand and provide an increased signal.This causes a substantial increase in the mean peak height compared tothe peak height when using unmodified primers.

REFERENCES

-   1 Wiedmann M. et al. PCR Methods and Applications 1994 3(4)S51-64-   2 Walker et al. Nucleic Acids Res. 1992. 20(7) 1691-1696-   3 Wroblewski J. et al. J. Clin. Microbiol. 2006:44(9):3306-3312-   4 Compton J. Nature 1991:350(6313):91-2-   5 Vincent M. et al. EMBO Rep. 2004 5(8) 795-800-   6 Notomi et al. Res. 2000 23 (12):E63.

1. A nucleic acid amplification method comprising steps of: a)performing nucleic acid amplification on a sample, using a first primerincluding at least one modified nucleotide (“modified primer”) and asecond primer, wherein the amplification provides a double strandednucleic acid comprising a first strand comprising the modified primerand a downstream amplified region; and a second strand; and b)incubating the double stranded nucleic acid of a) with a 5′ to 3′ doublestranded nucleic acid specific exonuclease which hydrolyses the secondstrand but does not hydrolyse the amplified region of the first strand,to provide a single stranded nucleic acid comprising the amplifiedregion of the first strand.
 2. The method of claim 1, further comprisingthe steps of: c) incubating the product of b) with a probe including alabel, wherein the probe specifically hybridises to the single strandednucleic acid; d) incubating the product of c) with a 5′ to 3′ doublestranded nucleic acid specific exonuclease which hydrolyses the probebut does not hydrolyse the amplified region of the first strand, whereinhydrolysis of the probe leads to a detectable change in the signal fromthe label; and e) detecting the change.
 3. The method of claim 2,wherein the exonucleases of step b) and step d) are the sameexonuclease.
 4. A nucleic acid amplification method comprising steps ofsteps of: i. incubating a sample with uracil-N-glycosylase; and ii.performing nucleic acid amplification on the product of i. using a firstprimer including at least one modified nucleotide, a second primer, anddUTP in the absence of dTTP, wherein the amplification provides a doublestranded nucleic acid comprising a first strand comprising the modifiedprimer and a downstream amplified region; and a second strand.
 5. Themethod of claim 4, further comprising a step of: iii. incubating thedouble stranded nucleic acid of ii. with a 5′ to 3′ double strandednucleic acid specific exonuclease which hydrolyses the second strand butdoes not hydrolyse the amplified region of the first strand, to providea single stranded nucleic acid comprising the amplified region of thefirst strand.
 6. The method of claim 4 or claim 5, further comprisingthe steps of: iv. incubating the product of iii. with a probe includinga label, wherein the probe specifically hybridises to the singlestranded nucleic acid; v. incubating the product of iv. with a 5′ to 3′double stranded nucleic acid specific exonuclease which hydrolyses theprobe but does not hydrolyse the amplified region of the first strand,wherein hydrolysis of the probe leads to a detectable change in thesignal from the label; and vi. detecting the change.
 7. The method ofclaim 6, wherein the exonucleases of step iii. and step v. are the sameexonuclease.
 8. The method of any preceding claim, wherein the nucleicacid amplification is achieved using PCR.
 9. The method of any precedingclaim, wherein the sample is a human sample.
 10. The method of any oneof claims 1-9, wherein the sample is a cellular sample.
 11. The methodof any one of claims 1-9, wherein the sample comprises purified nucleicacids.
 12. A first primer comprising the nucleotide sequence of SEQ IDNO: 1 or SEQ ID NO: 2, wherein nucleotides 1-3 or 1-4 are modifiednucleotides.
 13. A pair of primers comprising a first primer comprisingthe nucleotide sequence of SEQ ID NO: 1, wherein nucleotides 1-3 or 1-4are modified nucleotides; and a second primer comprising the nucleotidesequence of SEQ ID NO: 2, wherein the second primer is unmodified.
 14. Apair of primers comprising a first primer comprising the nucleotidesequence of SEQ ID NO: 2, wherein nucleotides 1-3 or 1-4 are modifiednucleotides; and a second primer comprising the nucleotide sequence ofSEQ ID NO: 1, wherein the second primer is unmodified.
 15. The firstprimer of claim 12 or the pair of primers of claim 13 or claim 14,wherein the modified nucleotides comprise phosphorothioate linkages. 16.A kit comprising a modified primer having at least one modifiednucleotide; and a 5′ to 3′ double stranded nucleic acid specificexonuclease.
 17. The kit of claim 16, further comprising a probeincluding a label.
 18. The method or kit of any one of claim 1-11 or16-17, wherein the at least one modified nucleotide comprises at leastone modified sugar moiety.
 19. The method or kit of claim 18, whereinthe at least one modified sugar moiety is a 2′-O-methyl sugar moiety.20. The method or kit of any one of claim 1-11 or 16-19, wherein the atleast one modified nucleotide comprises at least one modifiedinternucleoside linkage.
 21. The method or kit of claim 20, wherein theat least one modified internucleoside linkage is a phosphorothioatelinkage.
 22. The method or kit of any one of claim 1-11 or 16-21,wherein the at least one modified nucleotide comprises at least onemodified nucleobase.
 23. The method or kit of any one of claim 1-11 or16-22, wherein the modified primer comprises at least 2, at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9 orat least 10 modified nucleotides.
 24. The method or kit of any one ofclaim 1-11 or 16-23, wherein the modified primer comprises 3 or 4phosphorothioate linkages.
 25. The method or kit of any one of claim1-11 or 16-24, wherein the primers specifically hybridise to a Chlamydiatrachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasmagenitalium or methicillin resistant Staphylococcus aureus nucleic acid.26. The method or kit of any one of claim 1-11 or 16-25, wherein themodified primer is as defined in claim
 12. 27. The method or kit of anyone of claim 1-11 or 16-26, wherein the exonuclease is T7 exonuclease.28. The method or kit of any one of claim 1-11 or 16-27, wherein thelabel is an electrochemical label.
 29. The method or kit of any one ofclaim 1-11 or 16-28, wherein the electrochemical label is a ferrocenelabel.
 30. The method or kit of any one of claim 1-11 or 16-28, whereinthe labelled probe comprises a fluorescent label.
 31. A kit comprising amodified primer having at least one modified nucleotide, dUTP and UNG.32. The kit of claim 31, further comprising a 5′ to 3′ double strandednucleic acid specific exonuclease.
 33. The kit of claim 32, furthercomprising a probe including a label.
 34. The kit of any one of claims31-33, wherein the modified primer is as defined in claim 12.